Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatatcataagtcacattttatgcattccaactaaatatccttcaccgtaagagtcgaaatgaagaaaaactctgatcactgaaagttttcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTAC

Basic information

species Arabidopsis thaliana
transcript AT2G18230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G37790.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------------atatatcataagtcacattttatgcattccaactaaatatccttcaccgtaagagtcgaaatgaagaaaaact--ctgatcactgaaagttttcctc-------tctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTAC
                                                                                      |||   ||  | || |||||      | | || | | |   | |  |     |  | |   ||||| | ||||  || |  |  ||| ||| |  ||         |||||||||||  |||| ||||||||  |||| ||||| |||||||| ||||| |||||  |||| || ||||||||||||||||| ||||| || ||||| |
gtgtcgtttccattttctttcttgcactcctcttcttccattccatatgcttaatgtattagcaaaatgtgaaagactttcttttaatagggcagtattctcatttaccatttccaaatttatttctcattgctacctgtct-gtggtgaagcataactaactcactaacgaatgttctgatcaacccaacttagGTTGATCGTATTCTTTACTCATCAGTTGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTC

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------atatatcataagtcacattttat-------gcattccaactaaatatccttcaccgtaagagtcgaaatgaagaaaaact--ctgatcactgaaagttttcctc-------tctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTAC
                                                            | |||| | |       |||||        | ||||  | | |  ||     |   || |  | | | ||||| | ||||  || |  |  ||| ||  |  ||         |||||||||||  |||| ||||||||  | || ||||| |||||||| ||||| |||||  |||| || ||||||||||||||||| ||||| || ||||| |
gtgtggttgccattttcttgcattcctcttcttcatttccttatgcttgatgtatttgcaaaatatgaaagactttcttttaataggatagtattctcatttaccatttcgaagtttatgtct-gtactgaagcataactaactcactaacgaatgtgctgatcaacccaacttagGTTGATCGTATTCTTTACTCATCAGTAGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTC

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 3'ss of exon 3
atatatcataagtcacattttatgcattccaactaaatatcct-tcaccgtaagagtcgaaatgaagaaaaactctgatcactgaaagttttcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTAC
 | |  | ||  |  |  ||   |  || | |    |||||   |    ||| |   |  |||  | || |   || |  | || |  | | |     ||||||||||| ||||| ||||||||  |||| || || || ||||| ||||||||||||||||| |||||||||||||| ||||| |||||||||||| | |
tttttgcttatattgctgttatagtgttgctagattatatctgatttgtgtatgca-ctcaatatataagatagctaaagaatggagttctccaaaaatagGTTGATCGTGTTCTTTACTCATCAGTTGTTTATCCACATAACTATGGTTTCATCCCTCGAACCATCTGTGAAGACAGCGATCCTATGGATGTCCTGATTC

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ27219 (Selaginella moellendorffii), 3'ss of exon 3
atatatcataagtcacattttatgcattccaactaaatatccttcaccgtaagagtcgaaatgaagaaaaactctgatcactgaaagttttc---ctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTAC
                                                ||  || | ||   ||| ||| | | ||   |||     ||||    ||    |||||||  | || || ||||| ||  | ||||||||||||||||| |||||||| ||||| ||| | || |||||||  |||||| |||| ||| |||| |
------------------------------------------------gtttga-ttgaggagaacaaacattttggatacttcttatttttaaactgcgcagGTTGACAGGGTGCTGTACTCGTCGGTCGTGTACCCCCACAACTATGGTTTCATTCCTCGTACTCTGTGCGAAGACAACGATCCATTGGACGTCTTGGTCC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|164067498|gb|ES092633.1|ES092633
EST:     GTGGCCTTATTAAG                         GTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
genomic: GTGGCCTTATTAAGgtacagtgtt ... tcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
EST: gi|116390031|gb|EG432623.1|EG432623
EST:     AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG                         GTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
genomic: AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAGgtacagtgtt ... tcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
EST: gi|116443156|gb|EG485748.1|EG485748
EST:     AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG                         GTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
genomic: AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAGgtacagtgtt ... tcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
EST: gi|116390040|gb|EG432632.1|EG432632
EST:     AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG                         GTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
genomic: AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAGgtacagtgtt ... tcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
EST: gi|116443161|gb|EG485753.1|EG485753
EST:     AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG                         GTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
genomic: AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAGgtacagtgtt ... tcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
EST: gi|116390041|gb|EG432633.1|EG432633
EST:     AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG                         GTTGATCGCGTTCTATACTCATCCATTGTGTACCCCCACAACTACGGTTTC
genomic: AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAGgtacagtgtt ... tcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
EST: gi|116451434|gb|EG494026.1|EG494026
EST:     AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG                         GTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCTACAACTACGGTTTC
genomic: AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAGgtacagtgtt ... tcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
EST: gi|164019738|gb|ES130196.1|ES130196
EST:     GTACGAGCTAGACAAGAACAGTGGCCTTATTAAG                         GTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
genomic: GTACGAGCTAGACAAGAACAGTGGCCTTATTAAGgtacagtgtt ... tcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC
EST: gi|116451435|gb|EG494027.1|EG494027
EST:     AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAG                         GTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCTACAACTACGGTTTC
genomic: AAGGTGGAAAGGTTAAGTACGAGCTAGACAAGAACAGTGGCCTTATTAAGgtacagtgtt ... tcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accgtaagagtcgaaatgaagaaaaactctgatcactgaaagttttcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTAC
                          ctctgat  putative branch site (score: 4)
                                          ttttcctctct  putative PPT
                  aagaaaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatatcataagtcacattttatgcattccaactaaatatccttcaccgtaagagtcgaaatgaagaaaaactctgatcactgaaagttttcctctctagGTTGATCGCGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - atcataa
- - - - - - - - - - - - - - - aactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaaag